Let them fly what they want, I can't remember the last time I saw a shuttle in a PVP, and it's rare to see any fleet tier ships that look low level, even more so if they ARE Tier 1-4.
The second you start trying to tell people they can't fly or use things that are NOT broken or bugged, you know you're just trying too hard to control stuff.
If I queue up and find somebody like this on my team, sure it's annoying. But it's just an arena. And half the time the other side is a premade with nothing better to do anyway. The end scores will reflect the weakness on your team. If it matters so much, fly with some friends, limit your chances. If not it's just one more thing that we can't control and thus shouldn't waste time moaning about.